Hi all,
Can you please give write access to the scRNAseq package to Aaron Lun (
infinite.monkeys.with.keyboa...@gmail.com)?
Best,
Davide
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Hi Michael,
Thanks for looking into this.
Can you or someone with push permission to S4Vectors implement the workaround
that you mentioned?
Happy to create a pull request on Github if that helps.
We’re trying to solve this to fix the clusterExperiment package build on
Bioc-devel.
Thanks,
Dav
ps://travis-ci.org/epurdom/clusterExperiment/builds/126175973
Thanks,
Davide
On Mon, Apr 25, 2016 at 2:00 PM davide risso wrote:
> Thank you Michael and Martin for looking into this!
>
> Best,
> davide
>
>
> On Mon, Apr 25, 2016 at 1:49 PM Michael Lawrence <
> lawrence.m
age = package, resolve.msg =
> > resolve.msg)
> >
> > but I haven't quite got to the bottom of that. Also, I think these are
> both
> > different from but related to
> >
> >> suppressPackageStartupMessages(library(Statomica))
> > Error in .mergeMe
Dear list,
we are developing a new package that defines a class that builds on
SummarizedExperiment and also imports the CRAN package phylobase.
The class "Annotated" is defined both in the S4Vectors package (a
dependency of SummarizedExperiment) and in the RNeXML package (a dependency
of phyloba
tician after the experiment is done may be no
> more
> >> > than asking him to perform a post-mortem examination: he may be able
> to say
> >> > what the experiment died of. - Ronald Fisher
> >> >
> >> >
> >> >
> >> >
or
experimental data sharing.
Best,
davide
On Thu, Mar 3, 2016 at 12:50 PM Hervé Pagès wrote:
> Hi Davide,
>
> On 03/01/2016 02:25 PM, davide risso wrote:
> > Dear Bioc developers,
> >
> > I recently downloaded three publicly available single-cell RNA-seq
> dataset
Dear Bioc developers,
I recently downloaded three publicly available single-cell RNA-seq datasets
from the NCBI GEO/SRA repository and created an R package with some
gene-level summaries (read counts and FPKMs).
I'm currently using the package locally for my own tests, but I'm thinking
that this
Thanks Dan,
renaming the repository to RUVSeq solved the problem.
If you're still interested, there was no output from the script and the
value of $? was
$ echo $?
128
Best,
davide
On Fri, Jun 19, 2015 at 8:18 PM Dan Tenenbaum
wrote:
>
>
> - Original Message -----
>
Hi all,
I don't know why but this is not working for me.
I deleted the bridge for my RUVSeq package.
I forked Bioconductor-mirror/RUVSeq into drisso/RUVSeq-mirror
I then run:
$ git clone https://github.com/drisso/RUVSeq-mirror
$ bash ../update_remotes.sh
$ git checkout devel
error: pathspec 'de
pr. 23 seconds to implement. I agree
> it is not as clean from a design perspective, but you get 100% of the
> functionality and you can write a separate checker for the colData argument.
>
> On Thu, Jun 18, 2015 at 2:00 PM, davide risso
> wrote:
>
>> Thank you all for the respons
could put a DataFrame into a single column of
> > > another DataFrame. That actually solves a problem for me too (I don't
> > > intend to expose nested DataFrames to the users though).
> > >
> > >
> > > On 6/17/15 7:23 PM, Martin Morgan wrote:
>
Dear list,
I'm creating an R package to store RNA-seq data of a somewhat large project
in which I'm involved.
One of the initial goals is to compare different pre-processing pipelines,
hence I have multiple expression matrices corresponding to the same samples.
The SummarizedExperiment class seem
t use
> this "typical" approch -- is the "heatmap" function. Having tried to teach
> this function in several different classes, I have come to the conclusion
> that it is basically unusable by mortals. And I think the problem is that
> it tries to combine too many s
ion deleted]]
>>>
>>> _______
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>
>
>
> --
><http://www.av
tention to the various 'development version'
> flags on the page.
Yes. I also think they follow the link and just copy/paste the
biocLite() command without reading the rest of the page.
Best,
davide
On Wed, Sep 10, 2014 at 12:21 PM, Martin Morgan wrote:
> On 09/10/2014 11:37 AM, d
cents.
Davide
On Wed, Sep 10, 2014 at 11:19 AM, Martin Morgan wrote:
> On 09/10/2014 10:39 AM, davide risso wrote:
>>
>> I just wanted to add my support to Josef request.
>>
>> During the last few weeks I received several emails from users asking
>> me if I "p
CRAN packages for you
> without any trouble.
>
> ~G
>
>
>>
>> That's just my 2c :-).
>>
>> Cheers,
>> Josef
>>
>>
>> --
>> Josef Spidlen, Ph.D.
>> Staff Scientist, Terry Fox Laboratory, BC Cancer Agency
>> 675 Wes
Thank you Dan.
I should have looked at the time of my commit.
Best,
davide
On Tue, Apr 22, 2014 at 12:15 PM, Dan Tenenbaum wrote:
> Hi Davide,
>
> - Original Message -
>> From: "davide risso"
>> To: bioc-devel@r-project.org
>> Sent: Tuesday,
brary(knitr)
opts_chunk$set(dev="pdf", fig.align="center", cache=FALSE,
message=FALSE, out.width=".55\\textwidth", echo=TRUE,
results="markup", fig.show="hold")
options(width=60)
@
Am I missing something?
Best,
davide
--
Davide Risso, PhD
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